Vegetation loss is a primary cause of habitat degradation and results in a decline in reptile species abundance due to loss of refuge from predators and hot temperatures, and foraging opportunities. Texas horned lizards (Phrynosoma cornutum) have disappeared from many areas in Texas, especially from urbanized areas, probably in large part due to loss of suitable habitat. This species still occurs in some small towns in Texas that still contain suitable habitat. Long-term data from Kenedy and Karnes City, Texas indicate that when study sites experienced significant shrub and vegetation removal horned lizards declined by 79%. We hypothesize the decline was due to the degradation of the thermal landscape for these lizards. We determined the preferred temperature range (T_set25 −T_set75) of lizards at our study sites and took field measurements of body temperature (T_b). Temperature loggers were also placed in three microhabitats across our study sites. Shrubs and vegetation provided the highest quality thermal environment, especially for about 5 hours midday when temperatures in the open and buried under the surface in the open exceeded the lizards’ critical maximum temperature (CT_max) or were above their preferred temperature range. Horned lizard density was positively related to the thermal quality of the habitat across our sites. Texas horned lizards in these towns require a heterogeneous mix of closely spaced microhabitats and especially thermal refugia, such as shrubs and vegetation along fence lines and in open fields. Maintaining thermal refugia is one of the most important and practical conservation actions that can be taken to help small ectotherms persist in modified human landscapes and cope with increasing temperatures due to climate change.